def update_styles_for_annotations_in_folder(gc,
folderid,
workflow_kwargs,
recursive=True,
catch_exceptions=True,
monitor='',
verbose=True):
"""Update styles for all annotations in a folder recursively.
Parameters
----------
gc : girder_client.GirderClient
authenticated girder client
folderid : str
girder id of folder
workflow_kwargs : dict
kwargs to pass to Update styles for all annotations in a slide()
recursive : bool
do this recursively for subfolders?
catch_exceptions : bool
passed as-is to histomicstk.workflows.workflow_runner.Workflow_runner
monitor : str
text to prepend to printed statements
verbose : bool
print statements to screen?
Returns
-------
None
"""
# update annotation styles
workflow_kwargs.update({'gc': gc})
workflow_runner = Workflow_runner(
slide_iterator=Slide_iterator(
gc,
source_folder_id=folderid,
keep_slides=None,
),
workflow=update_styles_for_annotations_in_slide,
workflow_kwargs=workflow_kwargs,
recursive=recursive,
catch_exceptions=catch_exceptions,
monitorPrefix=monitor,
verbose=verbose,
)
workflow_runner.run()
def get_all_rois_from_folder_v2(
gc, folderid, get_all_rois_kwargs, monitor=''):
"""Get all rois in a girder folder using get_all_rois_from_slide_v2().
Parameters
----------
gc : girder_client.Girder_Client
authenticated girder client
folderid : str
girder id of folder
get_all_rois_kwargs : dict
kwargs to pass to get_all_rois_from_slide_v2()
monitor : str
monitor prefix
Returns
-------
None
"""
def _get_all_rois(slide_id, monitorPrefix, **kwargs):
sld = gc.get('/item/%s' % slide_id)
if "." not in sld['name']:
sld['name'] += "."
sldname = sld['name'][:sld['name'].find('.')].replace('/', '_#_')
return get_all_rois_from_slide_v2(
slide_id=slide_id, monitorprefix=monitorPrefix,
# encoding slide id makes things easier later
slide_name="%s_id-%s" % (sldname, slide_id),
**kwargs)
# update with params
get_all_rois_kwargs['gc'] = gc
# pull annotations for each slide in folder
workflow_runner = Workflow_runner(
slide_iterator=Slide_iterator(
gc, source_folder_id=folderid,
keep_slides=None,
),
workflow=_get_all_rois,
workflow_kwargs=get_all_rois_kwargs,
monitorPrefix=monitor
)
workflow_runner.run()
def revert_annotations_in_folder(gc,
folderid,
workflow_kwargs,
recursive=True,
monitor='',
verbose=True):
"""Revert all annotations in a folder recursively.
Parameters
----------
gc : girder_client.GirderClient
authenticated girder client
folderid : str
girder id of folder
workflow_kwargs : dict
kwargs to pass to revert_annotations_in_slide
recursive : bool
do this recursively for subfolders?
monitor : str
text to prepend to printed statements
verbose : bool
print statements to screen?
Returns
-------
None
"""
# update annotation styles
workflow_kwargs.update({'gc': gc})
workflow_runner = Workflow_runner(
slide_iterator=Slide_iterator(
gc,
source_folder_id=folderid,
keep_slides=None,
),
workflow=revert_annotations_in_slide,
workflow_kwargs=workflow_kwargs,
recursive=recursive,
monitorPrefix=monitor,
verbose=verbose,
)
workflow_runner.run()
def test_runner_using_Cellularity_detector_thresholding(self):
"""Test workflow runner for cellularity detection."""
# Init Cellularity_detector_thresholding
cdt = Cellularity_detector_thresholding(**cdt_params)
# Init workflow runner
workflow_runner = Workflow_runner(
slide_iterator=Slide_iterator(
gc, source_folder_id=SAMPLE_SOURCE_FOLDER_ID,
keep_slides=['TCGA-A1-A0SK-01Z-00-DX1_POST.svs', ],
# keep_slides=None,
),
workflow=cellularity_detection_workflow,
workflow_kwargs={
'gc': gc,
'cdo': cdt,
'destination_folder_id': SAMPLE_DESTINATION_FOLDER_ID,
'keep_existing_annotations': False, },
logging_savepath=cdt.logging_savepath,
monitorPrefix='test')
# Now run
workflow_runner.run()
def dump_annotations_locally(gc,
folderid,
local,
save_json=True,
save_sqlite=False,
dbcon=None,
callback=None,
callback_kwargs=None):
"""Dump annotations of folder and subfolders locally recursively.
This reproduces this tiered structure locally and (possibly) dumps
annotations there. Adapted from Lee A.D. Cooper
Parameters
-----------
gc : girder_client.GirderClient
authenticated girder client instance
folderid : str
girder id of source (base) folder
local : str
local path to dump annotations
save_json : bool
whether to dump annotations as json file
save_sqlite : bool
whether to save the backup into an sqlite database
dbcon : sqlalchemy.create_engine.connect() object
IGNORE THIS PARAMETER!! This is used internally.
callback : function
function to call that CAN accept AT LEAST the following params
- item: girder response with item information
- annotations: loaded annotations
- local: local directory
- monitorPrefix: string
- dbcon: sqlalchemy.create_engine.connect() object
You can just add kwargs at the end of your callback definition
for simplicity.
callback_kwargs : dict
kwargs to pass along to callback. DO NOT pass any of the parameters
item, annotations, local, monitorPrefix, or dbcon as these will be
internally passed. Just include any specific paremeters for the
callback. See parse_annotations_to_local_tables() above for
an example of a callback and the unir test of this function.
"""
callback_kwargs = callback_kwargs or {}
assert (save_json or save_sqlite), "must save results somehow!"
monitor = os.path.basename(local)
# get folder info
folder_info = gc.get("folder/%s" % folderid)
folder_info['folder_path'] = get_absolute_girder_folderpath(
gc=gc, folder_info=folder_info)
# connect to sqlite database -- only first stack does this
if save_sqlite and (dbcon is None):
db_path = os.path.join(local, folder_info['name'] + ".sqlite")
sql_engine = create_engine('sqlite:///' + db_path, echo=False)
dbcon = sql_engine.connect()
# save folder information json
if save_json:
print("%s: save folder info" % monitor)
savepath = os.path.join(local, folder_info['name'] + '.json')
with open(savepath, 'w') as fout:
json.dump(folder_info, fout)
# save folder info to sqlite
if save_sqlite:
_add_folder_to_sqlite(dbcon, folder_info)
# pull annotations for each slide in folder
workflow_runner = Workflow_runner(slide_iterator=Slide_iterator(
gc,
source_folder_id=folderid,
keep_slides=None,
),
workflow=dump_annotations_workflow,
workflow_kwargs={
'gc': gc,
'local': local,
'save_json': save_json,
'save_sqlite': save_sqlite,
'dbcon': dbcon,
'callback': callback,
'callback_kwargs': callback_kwargs,
},
monitorPrefix=monitor)
workflow_runner.run()
# for each subfolder, create a new folder locally and call self
for folder in gc.listFolder(parentId=folderid):
# create folder in local
new_folder = os.path.join(local, folder['name'])
os.mkdir(new_folder)
# call self with same prameters
dump_annotations_locally(gc=gc,
folderid=folder['_id'],
local=new_folder,
save_json=save_json,
save_sqlite=save_sqlite,
dbcon=dbcon,
callback=callback,
callback_kwargs=callback_kwargs)